data_X9L # _chem_comp.id X9L _chem_comp.name "5'-S-(2-{[(3-bromophenyl)methyl]amino}ethyl)-5'-thioadenosine" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H23 Br N6 O3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-10-26 _chem_comp.pdbx_modified_date 2025-03-28 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 495.393 _chem_comp.one_letter_code ? _chem_comp.three_letter_code X9L _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 8UQH _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal X9L C13 C1 C 0 1 N N S N N N -10.746 11.826 -76.286 2.807 2.022 -0.197 C13 X9L 1 X9L C17 C2 C 0 1 N N N N N N -12.955 16.116 -76.830 -2.381 1.195 1.187 C17 X9L 2 X9L C20 C3 C 0 1 Y N N N N N -12.411 19.715 -76.021 -6.101 0.788 1.010 C20 X9L 3 X9L C21 C4 C 0 1 Y N N N N N -12.893 19.892 -74.732 -6.591 -0.414 0.534 C21 X9L 4 X9L C22 C5 C 0 1 Y N N N N N -13.132 21.170 -74.248 -7.848 -0.470 -0.040 C22 X9L 5 X9L C24 C6 C 0 1 Y N N N N N -12.886 22.267 -75.060 -8.615 0.677 -0.138 C24 X9L 6 X9L C26 C7 C 0 1 Y N N N N N -12.164 20.811 -76.829 -6.868 1.934 0.913 C26 X9L 7 X9L C02 C8 C 0 1 Y N N N N N -10.641 6.813 -80.952 8.006 -2.824 0.260 C02 X9L 8 X9L C04 C9 C 0 1 Y N N N N N -10.827 5.879 -78.851 8.859 -0.779 0.907 C04 X9L 9 X9L C06 C10 C 0 1 Y N N N N N -10.386 8.177 -79.012 6.645 -0.834 0.293 C06 X9L 10 X9L C07 C11 C 0 1 Y N N N N N -10.398 8.092 -80.371 6.759 -2.212 0.045 C07 X9L 11 X9L C09 C12 C 0 1 Y N N N N N -9.999 10.174 -79.793 4.714 -1.644 -0.398 C09 X9L 12 X9L C11 C13 C 0 1 N N R N N N -10.053 9.961 -77.318 4.744 0.827 0.112 C11 X9L 13 X9L C14 C14 C 0 1 N N N N N N -11.107 12.966 -77.028 1.347 1.921 -0.641 C14 X9L 14 X9L C16 C15 C 0 1 N N N N N N -12.635 15.135 -75.702 -1.365 1.489 0.082 C16 X9L 15 X9L C19 C16 C 0 1 N N N N N N -12.145 18.309 -76.556 -4.734 0.847 1.641 C19 X9L 16 X9L C25 C17 C 0 1 Y N N N N N -12.402 22.088 -76.348 -8.125 1.878 0.339 C25 X9L 17 X9L C27 C18 C 0 1 N N S N N N -9.184 11.734 -76.154 3.702 2.444 -1.383 C27 X9L 18 X9L C29 C19 C 0 1 N N R N N N -8.837 11.044 -77.125 5.005 1.640 -1.175 C29 X9L 19 X9L N01 N1 N 0 1 N N N N N N -10.666 6.657 -82.395 8.180 -4.177 0.027 N01 X9L 20 X9L N03 N2 N 0 1 Y N N N N N -10.846 5.760 -80.171 9.015 -2.072 0.687 N03 X9L 21 X9L N05 N3 N 0 1 Y N N N N N -10.604 7.047 -78.278 7.710 -0.164 0.719 N05 X9L 22 X9L N08 N4 N 0 1 Y N N N N N -10.154 9.347 -80.839 5.545 -2.644 -0.374 N08 X9L 23 X9L N10 N5 N 0 1 Y N N N N N -10.135 9.465 -78.671 5.344 -0.504 0.006 N10 X9L 24 X9L N18 N6 N 0 1 N N N N N N -13.265 17.426 -76.284 -3.730 1.129 0.607 N18 X9L 25 X9L O12 O1 O 0 1 N N N N N N -11.145 10.580 -77.031 3.305 0.725 0.198 O12 X9L 26 X9L O28 O2 O 0 1 N N N N N N -8.829 11.034 -74.854 3.967 3.847 -1.336 O28 X9L 27 X9L O30 O3 O 0 1 N N N N N N -7.563 10.337 -76.823 6.115 2.523 -0.993 O30 X9L 28 X9L S15 S1 S 0 1 N N N N N N -10.979 14.434 -75.966 0.300 1.570 0.798 S15 X9L 29 X9L BR23 BR1 BR 0 0 N N N N N N -13.808 21.424 -72.443 -8.518 -2.114 -0.692 BR23 X9L 30 X9L H1 H1 H 0 1 N N N N N N -11.198 11.832 -75.283 2.906 2.732 0.624 H1 X9L 31 X9L H2 H2 H 0 1 N N N N N N -13.821 15.746 -77.399 -2.141 0.241 1.657 H2 X9L 32 X9L H3 H3 H 0 1 N N N N N N -12.085 16.198 -77.498 -2.345 1.987 1.935 H3 X9L 33 X9L H4 H4 H 0 1 N N N N N N -13.082 19.034 -74.105 -5.991 -1.309 0.610 H4 X9L 34 X9L H5 H5 H 0 1 N N N N N N -13.072 23.264 -74.689 -9.597 0.634 -0.586 H5 X9L 35 X9L H6 H6 H 0 1 N N N N N N -11.787 20.671 -77.831 -6.485 2.873 1.285 H6 X9L 36 X9L H7 H7 H 0 1 N N N N N N -10.996 5.008 -78.236 9.705 -0.205 1.254 H7 X9L 37 X9L H8 H8 H 0 1 N N N N N N -9.798 11.234 -79.850 3.677 -1.707 -0.694 H8 X9L 38 X9L H9 H9 H 0 1 N N N N N N -9.857 9.126 -76.629 5.139 1.355 0.981 H9 X9L 39 X9L H10 H10 H 0 1 N N N N N N -10.431 13.074 -77.889 1.039 2.865 -1.093 H10 X9L 40 X9L H11 H11 H 0 1 N N N N N N -12.142 12.860 -77.386 1.243 1.118 -1.370 H11 X9L 41 X9L H12 H12 H 0 1 N N N N N N -12.661 15.663 -74.737 -1.401 0.697 -0.665 H12 X9L 42 X9L H13 H13 H 0 1 N N N N N N -13.380 14.326 -75.697 -1.605 2.443 -0.388 H13 X9L 43 X9L H14 H14 H 0 1 N N N N N N -11.243 17.905 -76.072 -4.715 1.637 2.392 H14 X9L 44 X9L H15 H15 H 0 1 N N N N N N -11.985 18.362 -77.643 -4.510 -0.109 2.114 H15 X9L 45 X9L H16 H16 H 0 1 N N N N N N -12.211 22.945 -76.976 -8.723 2.774 0.263 H16 X9L 46 X9L H17 H17 H 0 1 N N N N N N -8.766 12.751 -76.151 3.233 2.176 -2.330 H17 X9L 47 X9L H18 H18 H 0 1 N N N N N N -8.736 11.610 -78.063 5.184 0.973 -2.018 H18 X9L 48 X9L H19 H19 H 0 1 N N N N N N -10.849 5.701 -82.624 7.437 -4.714 -0.289 H19 X9L 49 X9L H20 H20 H 0 1 N N N N N N -11.385 7.235 -82.780 9.045 -4.588 0.179 H20 X9L 50 X9L H21 H21 H 0 1 N N N N N N -14.092 17.786 -76.716 -3.951 1.979 0.110 H21 X9L 51 X9L H23 H23 H 0 1 N N N N N N -9.100 11.572 -74.120 4.525 4.167 -2.059 H23 X9L 52 X9L H24 H24 H 0 1 N N N N N N -6.866 10.973 -76.713 6.323 3.057 -1.772 H24 X9L 53 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal X9L N01 C02 SING N N 1 X9L C02 C07 DOUB Y N 2 X9L C02 N03 SING Y N 3 X9L N08 C07 SING Y N 4 X9L N08 C09 DOUB Y N 5 X9L C07 C06 SING Y N 6 X9L N03 C04 DOUB Y N 7 X9L C09 N10 SING Y N 8 X9L C06 N10 SING Y N 9 X9L C06 N05 DOUB Y N 10 X9L C04 N05 SING Y N 11 X9L N10 C11 SING N N 12 X9L C11 C29 SING N N 13 X9L C11 O12 SING N N 14 X9L C29 O30 SING N N 15 X9L C29 C27 SING N N 16 X9L O12 C13 SING N N 17 X9L C14 C13 SING N N 18 X9L C14 S15 SING N N 19 X9L C17 N18 SING N N 20 X9L C17 C16 SING N N 21 X9L C26 C25 DOUB Y N 22 X9L C26 C20 SING Y N 23 X9L C19 N18 SING N N 24 X9L C19 C20 SING N N 25 X9L C25 C24 SING Y N 26 X9L C13 C27 SING N N 27 X9L C27 O28 SING N N 28 X9L C20 C21 DOUB Y N 29 X9L S15 C16 SING N N 30 X9L C24 C22 DOUB Y N 31 X9L C21 C22 SING Y N 32 X9L C22 BR23 SING N N 33 X9L C13 H1 SING N N 34 X9L C17 H2 SING N N 35 X9L C17 H3 SING N N 36 X9L C21 H4 SING N N 37 X9L C24 H5 SING N N 38 X9L C26 H6 SING N N 39 X9L C04 H7 SING N N 40 X9L C09 H8 SING N N 41 X9L C11 H9 SING N N 42 X9L C14 H10 SING N N 43 X9L C14 H11 SING N N 44 X9L C16 H12 SING N N 45 X9L C16 H13 SING N N 46 X9L C19 H14 SING N N 47 X9L C19 H15 SING N N 48 X9L C25 H16 SING N N 49 X9L C27 H17 SING N N 50 X9L C29 H18 SING N N 51 X9L N01 H19 SING N N 52 X9L N01 H20 SING N N 53 X9L N18 H21 SING N N 54 X9L O28 H23 SING N N 55 X9L O30 H24 SING N N 56 # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor X9L SMILES ACDLabs 12.01 "Brc1cccc(c1)CNCCSCC1OC(n2cnc3c(N)ncnc32)C(O)C1O" X9L InChI InChI 1.06 "InChI=1S/C19H23BrN6O3S/c20-12-3-1-2-11(6-12)7-22-4-5-30-8-13-15(27)16(28)19(29-13)26-10-25-14-17(21)23-9-24-18(14)26/h1-3,6,9-10,13,15-16,19,22,27-28H,4-5,7-8H2,(H2,21,23,24)/t13-,15-,16-,19-/m1/s1" X9L InChIKey InChI 1.06 JGFTVBMOETWOQF-NVQRDWNXSA-N X9L SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSCCNCc4cccc(Br)c4)[C@@H](O)[C@H]3O" X9L SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CSCCNCc4cccc(Br)c4)[CH](O)[CH]3O" X9L SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(cc(c1)Br)CNCCSC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O" X9L SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(cc(c1)Br)CNCCSCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier X9L "SYSTEMATIC NAME" ACDLabs 12.01 "5'-S-(2-{[(3-bromophenyl)methyl]amino}ethyl)-5'-thioadenosine" X9L "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R},3~{R},4~{S},5~{S})-2-(6-aminopurin-9-yl)-5-[2-[(3-bromophenyl)methylamino]ethylsulfanylmethyl]oxolane-3,4-diol" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site X9L "Create component" 2023-10-26 RCSB X9L "Initial release" 2025-04-02 RCSB #